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* Clean up examples folders
* Use `snake_case` names
* Rename `nci_corrector` as `nci_fdtd_stability`
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approximation) (#2899)
* Macroscopic Maxwell solver: do not update fields in EB
* Correct unused variable
* Add test with macroscopic solver
* Add automated test
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* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
`.editorconfig`: isort options
https://github.com/PyCQA/isort/wiki/isort-Settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* move import os (mpl)
* move import yt (mpl)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleanup around matplotlib.use
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleaning: double np and lib
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Examples: Python ShellBang & Executable
Make sure that all PICMI scripts and all analysis Python scripts
in `Examples/` are:
- executable (`chmod a+x`)
- start with a shell-bang to `python3`
Now, all scripts can be run directly without a `python3 ...` prefix
and also default to the only right executable of Python on older
systems. (New systems always have a `python3` alias, too.)
* Revert a moved numpy
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* increase tolerance for single precision test
* reset checksum
* change ad['field'] into ad[('mesh','field')] or ad['boxlib','field'] in yt script
* update field access in several files
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_rz.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_2d.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_rz.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_2d.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_rz.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_2d.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi.py
* Update Examples/Tests/Langmuir/analysis_langmuir_multi.py
* Update Examples/Modules/boosted_diags/analysis_3Dbacktransformed_diag.py
* Update Examples/Modules/boosted_diags/analysis_3Dbacktransformed_diag.py
Co-authored-by: Tools <warpx@lbl.gov>
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* adding base implementation of the conformal solver
* adding some preprocessor directives
* qualifying the isnan's correctly
* getting rid of some unused fields
* computing S_stab on the fly
* using empty in length check
* Source/FieldSolver/FiniteDifferenceSolver/EvolveB.cpp
* replaced a looponcpu with a parallelfor
* trying to not pass lending/borrowing info by reference in evolveB
* passing data using dataPtr
* converting inds into a device vector
* simplifying some +=
* extracting the inds BaseFabs as DataPtr
* Revert "extracting the inds BaseFabs as DataPtr"
This reverts commit bc709d2fcaa347c119514de79a3f57169a05af65.
* implementing new way ogf handling cell extensions (gpu compatible)
* fixing some white spaces
* removed a typo
* made a function static
* tidying up
* tidying up
* getting rid of the rho vector
* moving the rho update to evolveE
* refectoring the cell extension
* small chenge in input parameters
* updating WarpX.H
* bug fix
* fixing another bug
* rotating the cube
* updated gitignore
* using the conformal soler in the cube test
* fixing the signature of a function
* trying to fix the setVal problem
* Revert "trying to fix the setVal problem"
This reverts commit c7d0e5e3709b730ff570183b2a6df5f587ca4640.
* trying to fix the setVal problem
* cleaning some comments
* removing an abort in device code
* Including geometric information in the external field initializer
* cleaned up the test
* moving the geometric data initialization before the external fields initialization
* changing way of saving info about intruded cells
* fixed some white spaces
* Using S_mod instead of S_red and S_enl
* substituting a std::vector with amrex::Array1D
* bug fix in the uint8_t -> coords maps
* Condensed ect cell info into one single MultiFab
* fixing some includes
* fixing some more includes
* fixed a typo
* making some functions available in gpu code
* using tilebox instead of validbox for the geometry initialization
* communicating the geometric info in the guard cells
* fixing the guard cells initialization for ect
* fixing an unused parameter
* fixing an unused parameter
* ignored some unused variables when EB is not supported
* cleaning up
* cleaning up
* ignored some unused variables when EB is not supported
* evolving rho just for ect
* handling some more unused variables
* removing some white spaces
* adding the rotated cube test
* removed some white spaces
* change cells into faces
* small fix in unused parameters
* fixed a comment
* for safety for now just initialize the geometric data when lev==maxLevel
* adding some preprocessor directives to isolate EB code
* updating Makefile stuff
* Improving the rotated cube test
* bug fix in mesh refinement
* fixing boundary conditions in rotated cube test
* deactivating MPI in rotated cube test
* activating mpi in test
* improving outputs of cells extension
* improved the documentation
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Removed some obsolete isnan's
* undone change to gitignore
* adding some missing AMREX_GPU_DEVICEs
* Changing some amrex::Real(0) into 0.
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Making some variables const
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Adding amrex:: to some ignore_unused
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Enhancing readability of some parallelfor's
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Removed some unecessary includes
* Fixing some tags
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixing the function CountExtFaces
* added a comment for Rhofield
* Fixed a typo in CountExtCells
* trying to remove accesses to private members in ComputeEdgeLengths
* making some functions public
* undoing some useless changes
* undoing some useless changes
* adding some AMREX_GPU_DEVICEs
* adding some unused variables
* adding some AMREX_GPU_DEVICEs to fix warnings
* fixing relative error
* Making several variables const
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixed a comment
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* changing some double to amrex::Real
* removing commented lines
* changing some double to amrex::Real
* removing commented lines
* inizialing nelems_x,y,z to avoid a warning
* Fixing number of cells
* Adding missing analysis routine in rotated cube test
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Making some variables constexpr
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Improving some reduce operations
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* reading time directly from the output
* fixed a few data types
* fixing another int
* Replacing or->||, and->&&, not->!
* Adding license info
* Adding a white space
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* removed some unused imports
* Moving the doxygen documentation
* Including AMReX_LayoutData.H
* removing some useless parameters
* adding ect solver to the doc
* Removing some useless reductions
* Small change for consistency
* Handling the resizing of arrays
* Handling correctly the resing of arrays
* Fixing some whitespaces
* Fixing an indentation
* Improving a comment
* Removed a useless initialization
* Renamed Rhofield to ECTRhofield
* Renamed Rhofield to ECTRhofield
* Added some if conditions to isolate some EB related code
* Improved some comments
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Made some functions not member of WarpX anymore
* Isolated some EB-only code
* Isolated some EB-only code
* Using the square brackets to access vectors
* Ignoring some unused variables
* Bug fix in initialization
* Removed a redundant if
* Using enumeration for connectivity and improved names
* Added a comment
* added a few comments
* Removed some useless template parameters
* Printing some info only in verbose mode
* Revert "Removed some useless template parameters"
This reverts commit 2c527980e6872c0212767c27f00e2b53ecbcfd0a.
* Fixed a bug with the neighbours enumeration
* Initializing geom data alsoo in the ghost cells
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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simulations (#1761)
* Update copyright notices
* allow specification of boundary potentials at runtime when using Dirichlet boundary conditions in the electrostatic solver (labframe)
* added parsing to boundary potentials specified at runtime to allow time dependence through a mathematical expression with t (time)
* updated to picmistandard 0.0.14 in order to set the electrostatic solver convergence threshold
* update docs
* various changes requested during PR review
* fixed issue causing old tests to break and added a new test for time varying boundary potentials
* possibly a fix for the failed time varying boundary condition test
* changed permission on the analysis file for the time varying BCs test
* switched to using yt for data analysis since h5py is not available
* made changes compatible with PR#1730; changed potential boundary setting routine to use the ParallelFor construct and set all boundaries in a single call
* fixed typo in computePhiRZ
* updated docs and fixed other minor typos
* fixed bug in returning from loop over dimensions when setting boundary potentials rather than continuing
* changed to setting potentials on domain boundaries rather than tilebox boundaries and changed picmi.py to accept boundary potentials
* now using domain.surroundingNodes() to get the proper boundary cells for the physical domain
* fixed typo in variable name specifying z-boundary potential
* changed boundary value parameter for Dirichlet BC to boundary.field_lo/hi and changed setPhiBC() to only loop over the grid points when a boundary value has changed
* switched specifying potential boundary values though individual inputs of the form boundary.potential_lo/hi_x/y/z and incorporated the new BC formalism through FieldBoundaryType::Periodic and FieldBoundaryType::PEC rather than Geom(0).isPeriodic(idim)
* removed incorrect check of whether the potential boundary values are already correct, also had to change the input to test space_charge_initialization_2d to comply with the new boundary condition input parameters and finally changed permissions to analysis_fields.py file for the embedded boundary test since it was failing
* remove line from WarpX-tests.ini that was incorrectly added during upstream merge
* changed input file for relativistic space charge initialization to new boundary condition specification
* fixed outdated comment and updated documentation to reflect that the Dirichlet BCs can also be specified when using the relativistic electrostatic field solver
* moved call to get domain boundaries inside the loop over levels
* cleaned up the code some by using domain.smallEnd and domain.bigEnd rather than lbound and ubound
* added check that a box contains boundary cells before launching a loop over that box cells to set the boundary conditions
Co-authored-by: Peter Scherpelz <peter.scherpelz@modernelectron.com>
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* Added staircased embedded boundaris to the YEE solver
* adding spherical resonating cavity test
* adding functions for fields initialization
* style adjustments
* fixing tabs
* fixed name of analysis script
* fixed name of analysis script
* fixed a few wrong preprocessor directives
* workaround for missing boost
* Revert "workaround for missing boost"
This reverts commit 601f9eb2ec6f8c2100304379b2bea1c6cf9d1851.
* another workaround for missing boost
* getting rid of boost by depending on c++17
* Removed a few unused variables
* adding USE_EB to addToCompileString for EB testing
* removed tabs
* fixing the inputs name for EB sphere test
* shortened the test
* zero padding the names of the images
* adjusted two for loops
* removed some unused variables
* improving the fields initialization
* removed the sphere test and implemented the cube test
* fixed edges lengths computation and added comments
* Fixed the case of all_regular geometries
* fixing a bug that was breaking some tests
* adding test folder
* fixed the default values for the EB cube test
* simplified the analysis script
* fixed cubic resonator default results
* inputting the plot file name from command line
* fixing the diag name
* Fixed a bug in edges initialization
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Adding comments to the staircased yee solver (thanks Remi)
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* fixed the cube resonator test
* removed an unused import
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Edoardo Zoni
Remi Lehe
Axel Huebl
Luca Fedeli
Lorenzo Giacomel
roelof-groenewald
